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[farmshare-discuss] matlab was:Re: job submission to barley machines

Abhik Lahiri alahiri at stanford.edu
Mon Sep 24 22:37:27 PDT 2012


Hi Alex, 
Thanks a lot for your reply. 
I'm using MATLAB R2011b (the default on the barley systems). On running 'module load MATLAB-MATLAB-R2012a' from my bash prompt (after ssh'ing into a barley machine), I get the following error: +(0):ERROR:0: Unable to locate a modulefile for 'MATLAB-MATLAB-R2012a' 


I'll try the -V flag. 


Thanks again! 
Abhik 

----- Original Message -----

From: "Alex Chekholko" <chekh at stanford.edu> 
To: "Abhik Lahiri" <alahiri at stanford.edu> 
Cc: "Open discussion for users of FarmShare" <farmshare-discuss at lists.stanford.edu> 
Sent: Monday, September 24, 2012 9:07:17 PM 
Subject: matlab was:Re: [farmshare-discuss] job submission to barley machines 

Hi Abhik, 

Which matlab are you using? 

I recommend the following: 
1) use 'module load MATLAB-MATLAB-R2012a' 
2) use the '-V' flag for qsub to pass the environment along 

I updated the example here: 
https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/MATLAB#example_single_matlab_file_run_via_qsub 

Regards, 
Alex 

On 9/24/12 8:26 PM, Abhik Lahiri wrote: 
> Hi, 
> 
> I am trying to submit bash scripts as jobs to the barley machines. The 
> command I am using is: qsub -cwd -o /dev/null -e /dev/null job1.script 
> 
> However, none of my jobs run. They script runs for a few seconds before 
> getting killed, and nothing is written to the output file in my script 
> too (I had earlier put filenames for the -o and -e but both the stdout 
> and stderr files were empty). 
> 
> My shell script starts matlab and runs a matlab script (the command used 
> is something like - unset DISPLAY; matlab > output_file << EOF; 
> matlab_task(arg1, arg2); exit; EOF - so, its the usual script to run a 
> matlab task and write the output to a file output_file). To debug this, 
> I ran a test job by ssh'ing directly into a barley and running this same 
> script, and it runs fine!! 
> 
> So, I wonder why the job scheduler is not able to run the script? Are 
> there some mandatory parameters I need to pass along with the qsub 
> command that I am missing here? The qsub command is run from my home dir 
> in /mnt/glusterfs, and output_file (in the matlab command above) is also 
> in my home dir in /mnt/glusterfs, so I am following the guidelines about 
> the location of input/output scripts here. 
> 
> Any help from someone will be greatly appreciated!! My research is on 
> hold right now because of this problem :( 
> 
> Thanks! 
> 
> Abhik 

-- 
Alex Chekholko chekh at stanford.edu 347-401-4860 

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